<?xml version="1.0"?>
<tool id="hyphy_fade" name="HyPhy-FADE" version="2.5.0+galaxy0">
  <description>: FUBAR* Approach to Directional Evolution (*Fast
  Unconstrained Bayesian Approximation)</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
    ln -s '$input_file' fade_input.fa &&
    ln -s '$input_nhx' fade_input.nhx &&
    @HYPHY_INVOCATIN@ fade
      --alignment `pwd`/fade_input.fa
      --tree `pwd`/fade_input.nhx
      --branches '$branches'
      --model '$substitutionmodel'
      --method '$posteriorEstimationMethod'
      --grid '$grid_points'
      --concentration_parameter '$concentration'
      --chains '$mcmc'
      --chain-length '$chain_length'
      --burn-in '$samples'
      --samples '$samples_per_chain'
      > '$fade_log'
    ]]></command>
  <inputs>
    <param name="input_file" type="data" format="fasta" label="Input amino acid FASTA file"/>
    <param name="input_nhx" type="data" format="nhx" label="Input rooted newick file"/>
    <param name="branches" type="select" label="Set of branches to test">
      <option value="1">All branches</option>
      <option value="2">Internal branches</option>
      <option value="3">Leaf branches</option>
      <option value="4">Unlabeled branches</option>
    </param>
    <param name="substitutionmodel" type="select" label="Substitution Model">
      <option value="1">LG (Generalist empirical model from Le and
      Gascuel 2008)</option>
      <option value="2">WAG (Generalist empirical model from Whelon
      and Goldman 2001)</option>
      <option value="3">JTT (Generalist empirical model from Jones,
      Taylor and Thornton 1996)</option>
      <option value="4">JC69 (Generalist empirical model with equal
      exhangeability rates among all amino acids)</option>
      <option value="5">mtMet (Specialist empirical model for
      metazoan mitochondrial genomes from Le, Dang and Le
      2007)</option>
      <option value="6">mtVer (Specialist empirical model for
      vertebrate mitochondrial gemones from Le, Dang and Le
      2007)</option>
      <option value="7">mtInv (Specialist empirical model for
      invertebrate mitochondrial genomes from Le, Dang and Le
      2007)</option>
      <option value="8">gcpREV (Specialist empirical model for
      green plant chloroplast genomes from Cox and Foster
      20013)</option>
      <option value="9">HIVBm (Specialist empirical model for
      between-host HIV sequences from Nickle et al. 2007)</option>
      <option value="10">HIVWm (Specialist empirical model for
      within-host HIV sequences from Nickle et al. 2007)</option>
      <option value="11">GTR (General time reversible model; 189
      estimated parameters)</option>
    </param>
    <param name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points"/>
    <param name="mcmc" type="integer" value="5" min="2" max="20" label="Number of MCMC chains"/>
    <param name="chain_length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain"/>
    <param name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in"/>
    <param name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain"/>
    <param name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior"/>
    <param name="branches" type="select" label="Set of branches to test">
      <option value="1">All branches</option>
      <option value="2">Internal branches</option>
      <option value="3">Leaf branches</option>
      <option value="4">Unlabeled branches</option>
    </param>
    <param name="posteriorEstimationMethod" type="select" label="Posterior estimation method">
      <option value="1">Metropolis-Hastings - Full
      Metropolis-Hastings MCMC algorithm (slowest, original 2013
      paper implementation)</option>
      <option value="2">Collapsed Gibbs - Collapsed Gibbs sampler
      (intermediate speed)</option>
      <option value="3">Variational Bayes - 0-th order Variational
      Bayes approximations (fastest, recommended default)</option>
    </param>
  </inputs>
  <outputs>
    <data name="fade_log" format="txt"/>
    <data name="fade_output" format="hyphy_json_results" from_work_dir="fade_input.fa.FADE.json"/>
  </outputs>
  <tests>
    <test>
      <param name="input_file" ftype="fasta" value="fade-in1.fa"/>
      <param name="input_nhx" ftype="nhx" value="fade-in1.nhx"/>
      <output name="fade_output" file="fade-out1.json" compare="sim_size"/>
    </test>
  </tests>
  <help><![CDATA[
FADE (FUBAR Approach to Directional Evolution) uses the same underlying algorithmic advances as impletented in FUBAR to apply Baysian MCMC accounting of parameter uncertiantiy to detect sites evolving under directional evolution in protien alignments. 
        ]]></help>
  <expand macro="citations">
    <citation type="doi">10.1093/molbev/msv022</citation>
  </expand>
</tool>